Arma Arma'ed Arma - Mission upload to server not working

[Wraith_last 0]

Gonna put the TLDR at the start: (Sorry if this problem is posted elsewhere, I did not see it)
When I make a mission and upload it to my server, I try to log in as normal and I get stuck in a perpetual loading screen
Details of note: When I click on my server, there is a field in the bottom left of the screen that shows the mission setup for the selected server. This field is empty.
Shortly before this started happening my game... Reset itself? I don't know how else to discribe it. You know when you create a new profile and you get a popup about Contact or whatever? All my saved addon settings for servers, Ops and all that were gone.

Now the whole story:
So I was updating a map I provide to my arma unit as a kinda side project and hobby.
I uploaded it as normal and when I went to test it, my game crashed as Arma does sometimes. I reopened the game and got the new profile thing of DLC popups appear and the game asked me if I wanted to do boot camp- It was odd but did not think too much of it.
I realised I had forgotten something when I was updating the map and went back and edited the part i had forgotten and uploaded it to the server.
I have a server with 40 slots but only make slots for 30 players. That means when my server shows up in the recent server list it should show 0/30 slots but it showed 0/40 slots in use. I then noticed the field on the bottom left was empty of mission presents. No map name or mission type was being shown.
I went back into eden and looked at the settings and found they were all reset back to the state they are in when you first make a mission.
I set up everything again, saved and out of paranoia I looked in the addon settings section and found they too were reset back to their respective mod defaults. When I tried to load the saved addon list I found that my saves were all gone too.
I rebuilt my server addon presets and then loaded it onto the server to be met with the same problem.

I figured that a mod was causing issues so to test I unloaded ALL mods and build a quick mission file with a single player and respawn, the basics of what you need to test new map, loaded the setting and configured the general and multiplayer setting. When I loaded it on the server I saw the same thing.
I have also lost "Add items to Zeus" option that I normally click on in the multiplayer tab and I no longer have the option to "Export as .pbo"
And that is where I am now. I can still test an MP game on my computer but anything I now build and try to upload onto the server does not work, not to mention the loss of options and functionalliy within Eden is annoying.
Anyone with ideas?